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megamerger |
The sequences can be very long. The program does a match of all sequence words of size 20 (by default). It then reduces this to the minimum set of overlapping matches by sorting the matches in order of size (largest size first) and then for each such match it removes any smaller matches that overlap. The result is a set of the longest ungapped alignments between the two sequences that do not overlap with each other. If the two sequences are identical in their region of overlap then there will be one region of match and no mismatches.
It should be possible to merge sequences that are Mega bytes long. Compare this with the program merger which does a more accurate alignment of more divergent sequences using the Needle and Wunsch algorithm but which uses much more memory.
The sequences should ideally be identical in their region of overlap. If there are any mismatches between the two sequences then megamerger will still attempt to create a merged sequence, but you should check that this is what you required.
A report of the actions of megamerger is written out. Any actions that require a choice between using regions of the two sequences where they have a mismatch is marked with the word WARNING!. The sequence in these regions is written out in uppercase. All other regions of the output sequence are written in lowercase.
Where there is a mismatch then the sequence that is chosen to supply the region of the mismatch in the final merged sequence is that sequence whose mismatch region is furthest from the start of end of the sequence.
% megamerger tembl:v00295 tembl:v00296 Merge two large overlapping nucleic acid sequences Word size [20]: output sequence [v00295.merged]: Output file [v00295.megamerger]: report |
Go to the input files for this example
Go to the output files for this example
Standard (Mandatory) qualifiers:
[-asequence] sequence Nucleotide sequence filename and optional
format, or reference (input USA)
[-bsequence] sequence Nucleotide sequence filename and optional
format, or reference (input USA)
-wordsize integer [20] Word size (Integer 2 or more)
[-outseq] seqout [
|
| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-asequence] (Parameter 1) |
Nucleotide sequence filename and optional format, or reference (input USA) | Readable sequence | Required |
| [-bsequence] (Parameter 2) |
Nucleotide sequence filename and optional format, or reference (input USA) | Readable sequence | Required |
| -wordsize | Word size | Integer 2 or more | 20 |
| [-outseq] (Parameter 3) |
Sequence filename and optional format (output USA) | Writeable sequence | <*>.format |
| [-outfile] (Parameter 4) |
Output file name | Output file | <*>.megamerger |
| Additional (Optional) qualifiers | Allowed values | Default | |
| -prefer | When a mismatch between the two sequence is discovered, one or other of the two sequences must be used to create the merged sequence over this mismatch region. The default action is to create the merged sequence using the sequence where the mismatch is closest to that sequence's centre. If this option is used, then the first sequence (seqa) will always be used in preference to the other sequence when there is a mismatch. | Boolean value Yes/No | No |
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| (none) | |||
ID V00295; SV 1; linear; genomic DNA; STD; PRO; 1500 BP.
XX
AC V00295;
XX
DT 09-JUN-1982 (Rel. 01, Created)
DT 07-JUL-1995 (Rel. 44, Last updated, Version 4)
XX
DE E. coli lacY gene (codes for lactose permease).
XX
KW membrane protein.
XX
OS Escherichia coli
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;
OC Enterobacteriaceae; Escherichia.
XX
RN [1]
RP 1-1500
RX DOI; 10.1038/283541a0.
RX PUBMED; 6444453.
RA Buechel D.E., Gronenborn B., Mueller-Hill B.;
RT "Sequence of the lactose permease gene";
RL Nature 283(5747):541-545(1980).
XX
CC lacZ is a beta-galactosidase and lacA is transacetylase.
CC KST ECO.LACY
XX
FH Key Location/Qualifiers
FH
FT source 1..1500
FT /organism="Escherichia coli"
FT /mol_type="genomic DNA"
FT /db_xref="taxon:562"
FT CDS <1..54
FT /codon_start=1
FT /transl_table=11
FT /note="reading frame (lacZ)"
FT /db_xref="GOA:P00722"
FT /db_xref="PDB:1BGL"
FT /db_xref="PDB:1BGM"
FT /db_xref="PDB:1DP0"
FT /db_xref="PDB:1F49"
FT /db_xref="PDB:1F4A"
FT /db_xref="PDB:1F4H"
FT /db_xref="PDB:1GHO"
FT /db_xref="PDB:1HN1"
FT /db_xref="PDB:1JYN"
FT /db_xref="PDB:1JYV"
FT /db_xref="PDB:1JYW"
FT /db_xref="PDB:1JYX"
FT /db_xref="PDB:1JYY"
[Part of this file has been deleted for brevity]
FT /db_xref="PDB:2CFP"
FT /db_xref="PDB:2CFQ"
FT /db_xref="UniProtKB/Swiss-Prot:P02920"
FT /protein_id="CAA23571.1"
FT /translation="MYYLKNTNFWMFGLFFFFYFFIMGAYFPFFPIWLHDINHISKSDT
FT GIIFAAISLFSLLFQPLFGLLSDKLGLRKYLLWIITGMLVMFAPFFIFIFGPLLQYNIL
FT VGSIVGGIYLGFCFNAGAPAVEAFIEKVSRRSNFEFGRARMFGCVGWALCASIVGIMFT
FT INNQFVFWLGSGCALILAVLLFFAKTDAPSSATVANAVGANHSAFSLKLALELFRQPKL
FT WFLSLYVIGVSCTYDVFDQQFANFFTSFFATGEQGTRVFGYVTTMGELLNASIMFFAPL
FT IINRIGGKNALLLAGTIMSVRIIGSSFATSALEVVILKTLHMFEVPFLLVGCFKYITSQ
FT FEVRFSATIYLVCFCFFKQLAMIFMSVLAGNMYESIGFQGAYLVLGLVALGFTLISVFT
FT LSGPGPLSLLRRQVNEVA"
FT CDS 1423..>1500
FT /transl_table=11
FT /note="reading frame (lacA)"
FT /db_xref="GOA:P07464"
FT /db_xref="PDB:1KQA"
FT /db_xref="PDB:1KRR"
FT /db_xref="PDB:1KRU"
FT /db_xref="PDB:1KRV"
FT /db_xref="UniProtKB/Swiss-Prot:P07464"
FT /protein_id="CAA23572.1"
FT /translation="MNMPMTERIRAGKLFTDMCEGLPEKR"
XX
SQ Sequence 1500 BP; 315 A; 342 C; 357 G; 486 T; 0 other;
ttccagctga gcgccggtcg ctaccattac cagttggtct ggtgtcaaaa ataataataa 60
ccgggcaggc catgtctgcc cgtatttcgc gtaaggaaat ccattatgta ctatttaaaa 120
aacacaaact tttggatgtt cggtttattc tttttctttt acttttttat catgggagcc 180
tacttcccgt ttttcccgat ttggctacat gacatcaacc atatcagcaa aagtgatacg 240
ggtattattt ttgccgctat ttctctgttc tcgctattat tccaaccgct gtttggtctg 300
ctttctgaca aactcgggct gcgcaaatac ctgctgtgga ttattaccgg catgttagtg 360
atgtttgcgc cgttctttat ttttatcttc gggccactgt tacaatacaa cattttagta 420
ggatcgattg ttggtggtat ttatctaggc ttttgtttta acgccggtgc gccagcagta 480
gaggcattta ttgagaaagt cagccgtcgc agtaatttcg aatttggtcg cgcgcggatg 540
tttggctgtg ttggctgggc gctgtgtgcc tcgattgtcg gcatcatgtt caccatcaat 600
aatcagtttg ttttctggct gggctctggc tgtgcactca tcctcgccgt tttactcttt 660
ttcgccaaaa cggatgcgcc ctcttctgcc acggttgcca atgcggtagg tgccaaccat 720
tcggcattta gccttaagct ggcactggaa ctgttcagac agccaaaact gtggtttttg 780
tcactgtatg ttattggcgt ttcctgcacc tacgatgttt ttgaccaaca gtttgctaat 840
ttctttactt cgttctttgc taccggtgaa cagggtacgc gggtatttgg ctacgtaacg 900
acaatgggcg aattacttaa cgcctcgatt atgttctttg cgccactgat cattaatcgc 960
atcggtggga aaaacgccct gctgctggct ggcactatta tgtctgtacg tattattggc 1020
tcatcgttcg ccacctcagc gctggaagtg gttattctga aaacgctgca tatgtttgaa 1080
gtaccgttcc tgctggtggg ctgctttaaa tatattacca gccagtttga agtgcgtttt 1140
tcagcgacga tttatctggt ctgtttctgc ttctttaagc aactggcgat gatttttatg 1200
tctgtactgg cgggcaatat gtatgaaagc atcggtttcc agggcgctta tctggtgctg 1260
ggtctggtgg cgctgggctt caccttaatt tccgtgttca cgcttagcgg ccccggcccg 1320
ctttccctgc tgcgtcgtca ggtgaatgaa gtcgcttaag caatcaatgt cggatgcggc 1380
gcgacgctta tccgaccaac atatcataac ggagtgatcg cattgaacat gccaatgacc 1440
gaaagaataa gagcaggcaa gctatttacc gatatgtgcg aaggcttacc ggaaaaaaga 1500
//
|
ID V00296; SV 1; linear; genomic DNA; STD; PRO; 3078 BP.
XX
AC V00296;
XX
DT 13-JUL-1983 (Rel. 03, Created)
DT 18-APR-2005 (Rel. 83, Last updated, Version 5)
XX
DE E. coli gene lacZ coding for beta-galactosidase (EC 3.2.1.23).
XX
KW galactosidase.
XX
OS Escherichia coli
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;
OC Enterobacteriaceae; Escherichia.
XX
RN [1]
RP 1-3078
RX PUBMED; 6313347.
RA Kalnins A., Otto K., Ruether U., Mueller-Hill B.;
RT "Sequence of the lacZ gene of Escherichia coli";
RL EMBO J. 2(4):593-597(1983).
XX
RN [2]
RX PUBMED; 3038536.
RA Zell R., Fritz H.J.;
RT "DNA mismatch-repair in Escherichia coli counteracting the hydrolytic
RT deamination of 5-methyl-cytosine residues";
RL EMBO J. 6(6):1809-1815(1987).
XX
CC Data kindly reviewed (18-MAY-1983) by U. Ruether
XX
FH Key Location/Qualifiers
FH
FT source 1..3078
FT /organism="Escherichia coli"
FT /mol_type="genomic DNA"
FT /db_xref="taxon:562"
FT CDS <1..3072
FT /transl_table=11
FT /note="galactosidase"
FT /db_xref="GOA:P00722"
FT /db_xref="PDB:1BGL"
FT /db_xref="PDB:1BGM"
FT /db_xref="PDB:1DP0"
FT /db_xref="PDB:1F49"
FT /db_xref="PDB:1F4A"
FT /db_xref="PDB:1F4H"
FT /db_xref="PDB:1GHO"
FT /db_xref="PDB:1HN1"
FT /db_xref="PDB:1JYN"
[Part of this file has been deleted for brevity]
gaggcccgca ccgatcgccc ttcccaacag ttgcgcagcc tgaatggcga atggcgcttt 180
gcctggtttc cggcaccaga agcggtgccg gaaagctggc tggagtgcga tcttcctgag 240
gccgatactg tcgtcgtccc ctcaaactgg cagatgcacg gttacgatgc gcccatctac 300
accaacgtaa cctatcccat tacggtcaat ccgccgtttg ttcccacgga gaatccgacg 360
ggttgttact cgctcacatt taatgttgat gaaagctggc tacaggaagg ccagacgcga 420
attatttttg atggcgttaa ctcggcgttt catctgtggt gcaacgggcg ctgggtcggt 480
tacggccagg acagtcgttt gccgtctgaa tttgacctga gcgcattttt acgcgccgga 540
gaaaaccgcc tcgcggtgat ggtgctgcgt tggagtgacg gcagttatct ggaagatcag 600
gatatgtggc ggatgagcgg cattttccgt gacgtctcgt tgctgcataa accgactaca 660
caaatcagcg atttccatgt tgccactcgc tttaatgatg atttcagccg cgctgtactg 720
gaggctgaag ttcagatgtg cggcgagttg cgtgactacc tacgggtaac agtttcttta 780
tggcagggtg aaacgcaggt cgccagcggc accgcgcctt tcggcggtga aattatcgat 840
gagcgtggtg gttatgccga tcgcgtcaca ctacgtctga acgtcgaaaa cccgaaactg 900
tggagcgccg aaatcccgaa tctctatcgt gcggtggttg aactgcacac cgccgacggc 960
acgctgattg aagcagaagc ctgcgatgtc ggtttccgcg aggtgcggat tgaaaatggt 1020
ctgctgctgc tgaacggcaa gccgttgctg attcgaggcg ttaaccgtca cgagcatcat 1080
cctctgcatg gtcaggtcat ggatgagcag acgatggtgc aggatatcct gctgatgaag 1140
cagaacaact ttaacgccgt gcgctgttcg cattatccga accatccgct gtggtacacg 1200
ctgtgcgacc gctacggcct gtatgtggtg gatgaagcca atattgaaac ccacggcatg 1260
gtgccaatga atcgtctgac cgatgatccg cgctggctac cggcgatgag cgaacgcgta 1320
acgcgaatgg tgcagcgcga tcgtaatcac ccgagtgtga tcatctggtc gctggggaat 1380
gaatcaggcc acggcgctaa tcacgacgcg ctgtatcgct ggatcaaatc tgtcgatcct 1440
tcccgcccgg tgcagtatga aggcggcgga gccgacacca cggccaccga tattatttgc 1500
ccgatgtacg cgcgcgtgga tgaagaccag cccttcccgg ctgtgccgaa atggtccatc 1560
aaaaaatggc tttcgctacc tggagagacg cgcccgctga tcctttgcga atacgcccac 1620
gcgatgggta acagtcttgg cggtttcgct aaatactggc aggcgtttcg tcagtatccc 1680
cgtttacagg gcggcttcgt ctgggactgg gtggatcagt cgctgattaa atatgatgaa 1740
aacggcaacc cgtggtcggc ttacggcggt gattttggcg atacgccgaa cgatcgccag 1800
ttctgtatga acggtctggt ctttgccgac cgcacgccgc atccagcgct gacggaagca 1860
aaacaccagc agcagttttt ccagttccgt ttatccgggc aaaccatcga agtgaccagc 1920
gaatacctgt tccgtcatag cgataacgag ctcctgcact ggatggtggc gctggatggt 1980
aagccgctgg caagcggtga agtgcctctg gatgtcgctc cacaaggtaa acagttgatt 2040
gaactgcctg aactaccgca gccggagagc gccgggcaac tctggctcac agtacgcgta 2100
gtgcaaccga acgcgaccgc atggtcagaa gccgggcaca tcagcgcctg gcagcagtgg 2160
cgtctggcgg aaaacctcag tgtgacgctc cccgccgcgt cccacgccat cccgcatctg 2220
accaccagcg aaatggattt ttgcatcgag ctgggtaata agcgttggca atttaaccgc 2280
cagtcaggct ttctttcaca gatgtggatt ggcgataaaa aacaactgct gacgccgctg 2340
cgcgatcagt tcacccgtgc accgctggat aacgacattg gcgtaagtga agcgacccgc 2400
attgacccta acgcctgggt cgaacgctgg aaggcggcgg gccattacca ggccgaagca 2460
gcgttgttgc agtgcacggc agatacactt gctgatgcgg tgctgattac gaccgctcac 2520
gcgtggcagc atcaggggaa aaccttattt atcagccgga aaacctaccg gattgatggt 2580
agtggtcaaa tggcgattac cgttgatgtt gaagtggcga gcgatacacc gcatccggcg 2640
cggattggcc tgaactgcca gctggcgcag gtagcagagc gggtaaactg gctcggatta 2700
gggccgcaag aaaactatcc cgaccgcctt actgccgcct gttttgaccg ctgggatctg 2760
ccattgtcag acatgtatac cccgtacgtc ttcccgagcg aaaacggtct gcgctgcggg 2820
acgcgcgaat tgaattatgg cccacaccag tggcgcggcg acttccagtt caacatcagc 2880
cgctacagtc aacagcaact gatggaaacc agccatcgcc atctgctgca cgcggaagaa 2940
ggcacatggc tgaatatcga cggtttccat atggggattg gtggcgacga ctcctggagc 3000
ccgtcagtat cggcggaatt ccagctgagc gccggtcgct accattacca gttggtctgg 3060
tgtcaaaaat aataataa 3078
//
|
# Report of megamerger of: V00295 and V00296 V00295 overlap starts at 1 V00296 overlap starts at 3019 Using V00296 1-3018 as the initial sequence Matching region V00295 1-60 : V00296 3019-3078 Length of match: 60 V00295 overlap ends at 60 V00296 overlap ends at 3078 Using V00295 61-1500 as the final sequence |
>V00295 V00295.1 E. coli lacY gene (codes for lactose permease). accatgattacggattcactggccgtcgttttacaacgtcgtgactgggaaaaccctggc gttacccaacttaatcgccttgcagcacatccccctttcgccagctggcgtaatagcgaa gaggcccgcaccgatcgcccttcccaacagttgcgcagcctgaatggcgaatggcgcttt gcctggtttccggcaccagaagcggtgccggaaagctggctggagtgcgatcttcctgag gccgatactgtcgtcgtcccctcaaactggcagatgcacggttacgatgcgcccatctac accaacgtaacctatcccattacggtcaatccgccgtttgttcccacggagaatccgacg ggttgttactcgctcacatttaatgttgatgaaagctggctacaggaaggccagacgcga attatttttgatggcgttaactcggcgtttcatctgtggtgcaacgggcgctgggtcggt tacggccaggacagtcgtttgccgtctgaatttgacctgagcgcatttttacgcgccgga gaaaaccgcctcgcggtgatggtgctgcgttggagtgacggcagttatctggaagatcag gatatgtggcggatgagcggcattttccgtgacgtctcgttgctgcataaaccgactaca caaatcagcgatttccatgttgccactcgctttaatgatgatttcagccgcgctgtactg gaggctgaagttcagatgtgcggcgagttgcgtgactacctacgggtaacagtttcttta tggcagggtgaaacgcaggtcgccagcggcaccgcgcctttcggcggtgaaattatcgat gagcgtggtggttatgccgatcgcgtcacactacgtctgaacgtcgaaaacccgaaactg tggagcgccgaaatcccgaatctctatcgtgcggtggttgaactgcacaccgccgacggc acgctgattgaagcagaagcctgcgatgtcggtttccgcgaggtgcggattgaaaatggt ctgctgctgctgaacggcaagccgttgctgattcgaggcgttaaccgtcacgagcatcat cctctgcatggtcaggtcatggatgagcagacgatggtgcaggatatcctgctgatgaag cagaacaactttaacgccgtgcgctgttcgcattatccgaaccatccgctgtggtacacg ctgtgcgaccgctacggcctgtatgtggtggatgaagccaatattgaaacccacggcatg gtgccaatgaatcgtctgaccgatgatccgcgctggctaccggcgatgagcgaacgcgta acgcgaatggtgcagcgcgatcgtaatcacccgagtgtgatcatctggtcgctggggaat gaatcaggccacggcgctaatcacgacgcgctgtatcgctggatcaaatctgtcgatcct tcccgcccggtgcagtatgaaggcggcggagccgacaccacggccaccgatattatttgc ccgatgtacgcgcgcgtggatgaagaccagcccttcccggctgtgccgaaatggtccatc aaaaaatggctttcgctacctggagagacgcgcccgctgatcctttgcgaatacgcccac gcgatgggtaacagtcttggcggtttcgctaaatactggcaggcgtttcgtcagtatccc cgtttacagggcggcttcgtctgggactgggtggatcagtcgctgattaaatatgatgaa aacggcaacccgtggtcggcttacggcggtgattttggcgatacgccgaacgatcgccag ttctgtatgaacggtctggtctttgccgaccgcacgccgcatccagcgctgacggaagca aaacaccagcagcagtttttccagttccgtttatccgggcaaaccatcgaagtgaccagc gaatacctgttccgtcatagcgataacgagctcctgcactggatggtggcgctggatggt aagccgctggcaagcggtgaagtgcctctggatgtcgctccacaaggtaaacagttgatt gaactgcctgaactaccgcagccggagagcgccgggcaactctggctcacagtacgcgta gtgcaaccgaacgcgaccgcatggtcagaagccgggcacatcagcgcctggcagcagtgg cgtctggcggaaaacctcagtgtgacgctccccgccgcgtcccacgccatcccgcatctg accaccagcgaaatggatttttgcatcgagctgggtaataagcgttggcaatttaaccgc cagtcaggctttctttcacagatgtggattggcgataaaaaacaactgctgacgccgctg cgcgatcagttcacccgtgcaccgctggataacgacattggcgtaagtgaagcgacccgc attgaccctaacgcctgggtcgaacgctggaaggcggcgggccattaccaggccgaagca gcgttgttgcagtgcacggcagatacacttgctgatgcggtgctgattacgaccgctcac gcgtggcagcatcaggggaaaaccttatttatcagccggaaaacctaccggattgatggt agtggtcaaatggcgattaccgttgatgttgaagtggcgagcgatacaccgcatccggcg cggattggcctgaactgccagctggcgcaggtagcagagcgggtaaactggctcggatta gggccgcaagaaaactatcccgaccgccttactgccgcctgttttgaccgctgggatctg ccattgtcagacatgtataccccgtacgtcttcccgagcgaaaacggtctgcgctgcggg acgcgcgaattgaattatggcccacaccagtggcgcggcgacttccagttcaacatcagc cgctacagtcaacagcaactgatggaaaccagccatcgccatctgctgcacgcggaagaa ggcacatggctgaatatcgacggtttccatatggggattggtggcgacgactcctggagc ccgtcagtatcggcggaattccagctgagcgccggtcgctaccattaccagttggtctgg tgtcaaaaataataataaccgggcaggccatgtctgcccgtatttcgcgtaaggaaatcc attatgtactatttaaaaaacacaaacttttggatgttcggtttattctttttcttttac ttttttatcatgggagcctacttcccgtttttcccgatttggctacatgacatcaaccat atcagcaaaagtgatacgggtattatttttgccgctatttctctgttctcgctattattc caaccgctgtttggtctgctttctgacaaactcgggctgcgcaaatacctgctgtggatt attaccggcatgttagtgatgtttgcgccgttctttatttttatcttcgggccactgtta caatacaacattttagtaggatcgattgttggtggtatttatctaggcttttgttttaac gccggtgcgccagcagtagaggcatttattgagaaagtcagccgtcgcagtaatttcgaa tttggtcgcgcgcggatgtttggctgtgttggctgggcgctgtgtgcctcgattgtcggc atcatgttcaccatcaataatcagtttgttttctggctgggctctggctgtgcactcatc ctcgccgttttactctttttcgccaaaacggatgcgccctcttctgccacggttgccaat gcggtaggtgccaaccattcggcatttagccttaagctggcactggaactgttcagacag ccaaaactgtggtttttgtcactgtatgttattggcgtttcctgcacctacgatgttttt gaccaacagtttgctaatttctttacttcgttctttgctaccggtgaacagggtacgcgg gtatttggctacgtaacgacaatgggcgaattacttaacgcctcgattatgttctttgcg ccactgatcattaatcgcatcggtgggaaaaacgccctgctgctggctggcactattatg tctgtacgtattattggctcatcgttcgccacctcagcgctggaagtggttattctgaaa acgctgcatatgtttgaagtaccgttcctgctggtgggctgctttaaatatattaccagc cagtttgaagtgcgtttttcagcgacgatttatctggtctgtttctgcttctttaagcaa ctggcgatgatttttatgtctgtactggcgggcaatatgtatgaaagcatcggtttccag ggcgcttatctggtgctgggtctggtggcgctgggcttcaccttaatttccgtgttcacg cttagcggccccggcccgctttccctgctgcgtcgtcaggtgaatgaagtcgcttaagca atcaatgtcggatgcggcgcgacgcttatccgaccaacatatcataacggagtgatcgca ttgaacatgccaatgaccgaaagaataagagcaggcaagctatttaccgatatgtgcgaa ggcttaccggaaaaaaga |
A merged sequence is written out.
Where there has been a mismatch between the two sequences, the merged sequence is written out in uppercase and the sequence whose mismatch region is furthest from the edges of the sequence is used in the merged sequence.
The name and description of the first input sequence is used for the name and description of the output sequence.
A report of the merger is written out.
| Program name | Description |
|---|---|
| cons | Creates a consensus from multiple alignments |
| merger | Merge two overlapping sequences |
Compare this with the program merger which does a more accurate alignment of more divergent sequences using the Needle and Wunsch algorithm but which uses much more memory.
A graphical dotplot of the matches used in this merge can be displayed using the program dotpath.